Dominant optic atrophy (DOA) is the most common hereditary optic neuropathy. Although DOA is caused by mutations in several genes, there are still many cases that have not been diagnosed or misdiagnosed. Herein, we present a large family of 11 patients with DOA. To identify potential pathogenic mutations, whole exome sequencing (WES) was performed on the proband, a 35-year-old woman. WES revealed a novel pathogenic mutation (c.524T>C, p.F175S) in the AFG3L2 intermembrane space domain, rather than in the ATPase domain, which is the hot mutation region associated with most of the previously reported DOA cases. Functional studies on skin fibroblasts generated from patients and HEK293T cells showed that the mutation may impair mitochondrial function and decrease the ability of AFG3L2 protein to enter the mitochondrial inner membrane. In addition, this novel mutation led to protein degradation and reduced the stability of the AFG3L2 protein, which appeared to be associated with the proteasome-ubiquitin pathway.